Sat, 24 Aug 2019

Package RcppExamples updated to version 0.1.9 with previous version 0.1.8 dated 2016-11-24

Title: Examples using 'Rcpp' to Interface R and C++
Description: Examples for Seamless R and C++ integration The 'Rcpp' package contains a C++ library that facilitates the integration of R and C++ in various ways. This package provides some usage examples. Note that the documentation in this package currently does not cover all the features in the package. The site <http://gallery.rcpp.org> regroups a large number of examples for 'Rcpp'.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppExamples versions 0.1.8 dated 2016-11-24 and 0.1.9 dated 2019-08-24

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Package SimBIID updated to version 0.1.1 with previous version 0.1.0 dated 2019-08-23

Title: Simulation-Based Inference Methods for Infectious Disease Models
Description: Provides some code to run simulations of state-space models, and then use these in the Approximate Bayesian Computation Sequential Monte Carlo (ABC-SMC) algorithm of Toni et al. (2009) <doi:10.1098/rsif.2008.0172> and a bootstrap particle filter based particle Markov chain Monte Carlo (PMCMC) algorithm (Andrieu et al., 2010 <doi:10.1111/j.1467-9868.2009.00736.x>). Also provides functions to plot and summarise the outputs.
Author: Trevelyan J. McKinley [aut, cre], Stefan Widgren [aut] (Author of 'R/mparse.R'), Pavol Bauer [cph] (R/mparse.R), Robin Eriksson [cph] (R/mparse.R), Stefan Engblom [cph] (R/mparse.R)
Maintainer: Trevelyan J. McKinley <t.mckinley@exeter.ac.uk>

Diff between SimBIID versions 0.1.0 dated 2019-08-23 and 0.1.1 dated 2019-08-24

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Package matrixsampling updated to version 2.0.0 with previous version 1.1.0 dated 2018-02-21

Title: Simulations of Matrix Variate Distributions
Description: Provides samplers for various matrix variate distributions: Wishart, inverse-Wishart, normal, t, inverted-t, Beta type I, Beta type II, Gamma, confluent hypergeometric. Allows to simulate the noncentral Wishart distribution without the integer restriction on the degrees of freedom.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>

Diff between matrixsampling versions 1.1.0 dated 2018-02-21 and 2.0.0 dated 2019-08-24

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New package lax with initial version 1.0.0
Package: lax
Title: Loglikelihood Adjustment for Extreme Value Models
Version: 1.0.0
Date: 2019-08-24
Authors@R: c( person(c("Paul", "J."), "Northrop", email = "p.northrop@ucl.ac.uk", role = c("aut", "cre", "cph")), person("Camellia", "Yin", role = c("aut", "cph")) )
Description: Performs adjusted inferences based on model objects fitted, using maximum likelihood estimation, by the extreme value analysis packages 'evd' <https://cran.r-project.org/package=evd>, 'evir' <https://cran.r-project.org/package=evir>, 'extRemes' <https://cran.r-project.org/package=extRemes>, 'fExtremes' <https://cran.r-project.org/package=fExtremes>, 'ismev' <https://cran.r-project.org/package=ismev>, 'POT' <https://cran.r-project.org/package=POT> and 'texmex' <https://cran.r-project.org/package=texmex>. Adjusted standard errors and an adjusted loglikelihood are provided, using the 'chandwich' package <https://cran.r-project.org/package=chandwich> and the object-oriented features of the 'sandwich' package <https://cran.r-project.org/package=sandwich>. The adjustment is based on a robust sandwich estimator of the parameter covariance matrix, based on the methodology in Chandler and Bate (2007) <doi:10.1093/biomet/asm015>. This can be used for cluster correlated data when interest lies in the parameters of the marginal distributions, or for performing inferences that are robust to certain types of model misspecification. Univariate extreme value models, including regression models, are supported.
Imports: chandwich, graphics, methods, numDeriv, revdbayes, sandwich, stats, utils
License: GPL (>= 2)
LazyData: TRUE
Encoding: UTF-8
Depends: R (>= 3.3.0)
RoxygenNote: 6.1.1
Suggests: distillery, evd, evir, extRemes, fExtremes, ismev, knitr, POT, rmarkdown, testthat, texmex
VignetteBuilder: knitr
URL: http://github.com/paulnorthrop/lax
BugReports: http://github.com/paulnorthrop/lax/issues
NeedsCompilation: no
Packaged: 2019-08-24 20:49:26 UTC; paul
Author: Paul J. Northrop [aut, cre, cph], Camellia Yin [aut, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Repository: CRAN
Date/Publication: 2019-08-24 22:00:05 UTC

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Package solitude updated to version 0.2.0 with previous version 0.1.3 dated 2019-06-05

Title: An Implementation of Isolation Forest
Description: Isolation forest is anomaly detection method introduced by the paper Isolation based Anomaly Detection (Liu, Ting and Zhou <doi:10.1145/2133360.2133363>).
Author: Komala Sheshachala Srikanth [aut, cre]
Maintainer: Komala Sheshachala Srikanth <sri.teach@gmail.com>

Diff between solitude versions 0.1.3 dated 2019-06-05 and 0.2.0 dated 2019-08-24

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Package ijtiff updated to version 2.0.3 with previous version 2.0.2 dated 2019-07-06

Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users. Currently the only such package with read and write support for TIFF files with floating point (real-numbered) pixels, and the only package that can correctly import TIFF files that were saved from 'ImageJ' and write TIFF files than can be correctly read by 'ImageJ' <https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>), Kent Johnson [aut], Simon Urbanek [ctb], Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>), Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>), Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>

Diff between ijtiff versions 2.0.2 dated 2019-07-06 and 2.0.3 dated 2019-08-24

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Package BANOVA updated to version 1.1.4 with previous version 1.1.3 dated 2019-07-21

Title: Hierarchical Bayesian ANOVA Models
Description: It covers several Bayesian Analysis of Variance (BANOVA) models used in analysis of experimental designs in which both within- and between- subjects factors are manipulated. They can be applied to data that are common in the behavioral and social sciences. The package includes: Hierarchical Bayes ANOVA models with normal response, t response, Binomial (Bernoulli) response, Poisson response, ordered multinomial response and multinomial response variables. All models accommodate unobserved heterogeneity by including a normal distribution of the parameters across individuals. Outputs of the package include tables of sums of squares, effect sizes and p-values, and tables of predictions, which are easily interpretable for behavioral and social researchers. The floodlight analysis and mediation analysis based on these models are also provided. BANOVA uses 'Stan' and 'JAGS' as the computational platform.
Author: Chen Dong, Michel Wedel
Maintainer: Chen Dong <cdong@math.umd.edu>

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Package sommer updated to version 4.0.4 with previous version 4.0.1 dated 2019-07-02

Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using i.e. the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>

Diff between sommer versions 4.0.1 dated 2019-07-02 and 4.0.4 dated 2019-08-24

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Package randomizeBE updated to version 0.3-5 with previous version 0.3-4 dated 2018-06-20

Title: Create a Random List for Crossover Studies
Description: Contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.
Author: D. Labes
Maintainer: D. Labes <detlewlabes@gmx.de>

Diff between randomizeBE versions 0.3-4 dated 2018-06-20 and 0.3-5 dated 2019-08-24

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Package cosa updated to version 2.0.0 with previous version 1.2.2 dated 2019-05-09

Title: Bound Constrained Optimal Sample Allocation
Description: Implements bound constrained optimal sample allocation (BCOSA) framework described in Bulus & Dong (2019) <doi:10.1080/00220973.2019.1636197> for power analysis of multilevel regression discontinuity designs (MRDDs) and multilevel randomized trials (MRTs) with continuous outcomes. Separate tools for statistical power and minimum detectable effect size computations are provided.
Author: Metin Bulus [aut, cre], Nianbo Dong [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

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New package ShiftShareSE with initial version 1.0.0
Package: ShiftShareSE
Title: Inference in Regressions with Shift-Share Structure
Version: 1.0.0
Authors@R: c(person(given = "Michal", family = "Kolesár", role = c("aut", "cre"), email = "kolesarmi@googlemail.com", comment = c(ORCID = "0000-0002-2482-7796")), person(given = "Eduardo", family = "Morales", role = "ctb", email = "ecmorale@princeton.edu"), person(given = "Rodrigo", family = "Adão", role = "ctb", email = "rodrigo.adao@chicagobooth.edu"))
Description: Provides confidence intervals in least-squares regressions when the variable of interest has a shift-share structure, and in instrumental variables regressions when the instrument has a shift-share structure. The confidence intervals implement the AKM and AKM0 methods developed in Adão, Kolesár, and Morales (2019) <doi:10.1093/qje/qjz025>.
Depends: R (>= 3.5.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
Suggests: testthat (>= 2.1.0), knitr, rmarkdown, AER, spelling, formatR
Imports: Formula
RoxygenNote: 6.1.1
URL: https://github.com/kolesarm/ShiftShareSE
Language: en-US
BugReports: https://github.com/kolesarm/ShiftShareSE/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-24 14:05:09 UTC; kolesarm
Author: Michal Kolesár [aut, cre] (<https://orcid.org/0000-0002-2482-7796>), Eduardo Morales [ctb], Rodrigo Adão [ctb]
Maintainer: Michal Kolesár <kolesarmi@googlemail.com>
Repository: CRAN
Date/Publication: 2019-08-24 15:00:02 UTC

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New package PostcodesioR with initial version 0.1.1
Package: PostcodesioR
Type: Package
Title: API Wrapper Around 'Postcodes.io'
Version: 0.1.1
Authors@R: c(person("Eryk", "Walczak", email = "eryk.j.walczak@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-8724-462X")), person("Claudia", "Vitolo", role = "rev", comment = c(ORCID = "0000-0002-4252-1176")), person("Robin", "Lovelace", role = "rev", comment = c(ORCID = "0000-0001-5679-6536")))
Maintainer: Eryk Walczak <eryk.j.walczak@gmail.com>
Description: Free UK geocoding using data from Office for National Statistics. It is using several functions to get information about post codes, outward codes, reverse geocoding, nearest post codes/outward codes, validation, or randomly generate a post code. API wrapper around <https://postcodes.io>.
License: GPL-3
URL: https://github.com/ropensci/PostcodesioR/
LazyData: TRUE
Depends: R (>= 3.1)
Imports: httr
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, testthat, covr
VignetteBuilder: knitr
BugReports: https://github.com/ropensci/PostcodesioR/issues
NeedsCompilation: no
Packaged: 2019-08-23 19:29:44 UTC; root
Author: Eryk Walczak [aut, cre] (<https://orcid.org/0000-0001-8724-462X>), Claudia Vitolo [rev] (<https://orcid.org/0000-0002-4252-1176>), Robin Lovelace [rev] (<https://orcid.org/0000-0001-5679-6536>)
Repository: CRAN
Date/Publication: 2019-08-24 14:20:09 UTC

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Package oompaBase updated to version 3.2.9 with previous version 3.2.8 dated 2019-05-06

Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be preloaded in order for the basic tools in the OOMPA (Object-Oriented Microarray and Proteomics Analysis) project to be defined and loaded. It also includes vectorized operations for row-by-row means, variances, and t-tests. Finally, it provides new color schemes. Details on the packages in the OOMPA project can be found at <http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>

Diff between oompaBase versions 3.2.8 dated 2019-05-06 and 3.2.9 dated 2019-08-24

 DESCRIPTION             |    8 ++++----
 MD5                     |   16 ++++++++--------
 NAMESPACE               |    5 +++--
 R/b02-colorSchemes.R    |   10 ++++++++++
 inst/doc/oompa.R        |   18 +++++++++++-------
 inst/doc/oompa.Rnw      |    8 +++++---
 inst/doc/oompa.pdf      |binary
 man/z02-colorSchemes.Rd |    3 +++
 vignettes/oompa.Rnw     |    8 +++++---
 9 files changed, 49 insertions(+), 27 deletions(-)

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New package irtplay with initial version 1.0.0
Package: irtplay
Type: Package
Title: Evaluation of Model-Data Fit in Item Response Theory (IRT) and Useful Functions Related to IRT
Version: 1.0.0
Description: Examine the IRT model-data fit on item-level in different ways as well as provide useful functions related to unidimensional item response theory (IRT). In terms of assessing the IRT model-data fit, one of distinguished features of this package is that it gives not only well-known item fit statistics (e.g., chi-square, infit and oufit statistics (Ames & Penfield (2015) <doi:10.1111/emip.12067>)) but also graphical displays to look at residuals between between the observed data and model-based predictions (Hambleton, Swaminathan, & Rogers (1991, ISBN:9780803936478)). More evaluation methods will be included in the future updated version. In addition to the evaluation of IRT model-data fit, there are several useful functions such as estimating proficiency parameters, calibrating item parameters given the fixed effects (aka. ability values) (Baker & Kim (2004, ISBN:9780824758257)), computing asymptotic variance-covariance matrices of item parameter estimates (Li & Lissitz (2004) <doi:10.1111/j.1745-3984.2004.tb01109.x>), importing item and/or ability parameters from popular IRT software, generating simulated data, computing the conditional distribution of observed scores using the Lord-Wingersky recursion formula (Lord & Wingersky (1984) <doi:10.1207/s15324818ame1002_1>), computing item and test information functions, computing item and test characteristic curve functions, and plotting item and test characteristic curves and item and test information functions.
Depends: R (>= 3.4)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Imports: stats, statmod, utils, reshape2, dplyr, tidyr, purrr, ggplot2, rlang, gridExtra, parallel, pbapply,
Authors@R: c(person("Hwanggyu", "Lim", email="hglim83@gmail.com", role=c("aut", "cre")), person("Craig S.", "Wells", email="cswells@educ.umass.edu ", rol="ctb") )
RoxygenNote: 6.1.1
Suggests: mirt
NeedsCompilation: no
Packaged: 2019-08-23 20:29:30 UTC; kijja
Author: Hwanggyu Lim [aut, cre], Craig S. Wells [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-24 14:20:03 UTC

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New package HCD with initial version 0.1
Package: HCD
Type: Package
Title: Hierarchical Community Detection by Recursive Partitioning
Version: 0.1
Date: 2019-08-02
Author: Tianxi Li, Lihua Lei, Sharmodeep Bhattacharyya, Purnamrita Sarkar, Peter Bickel, and Elizaveta Levina
Maintainer: Tianxi Li <tianxili@virginia.edu>
Description: Hierarchical community detection on networks by a recursive spectral partitioning strategy, which is shown to be effective and efficient in Li, Lei, Bhattacharyya, Sarkar, Bickel, and Levina (2018) <arXiv:1810.01509>. The package also includes a data generating function for a binary tree stochastic block model, a special case of stochastic block model that admits hierarchy between communities.
License: GPL (>= 2)
Imports: Matrix, stats, methods, randnet, RSpectra, irlba, data.tree, data.table,stringr,dendextend
NeedsCompilation: no
Packaged: 2019-08-23 16:51:15 UTC; tianxili
Repository: CRAN
Date/Publication: 2019-08-24 14:10:02 UTC

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Package crone updated to version 0.1.1 with previous version 0.1.0 dated 2019-07-27

Title: Structural Crystallography in 1d
Description: Functions to carry out the most important crystallographic calculations for crystal structures made of 1d Gaussian-shaped atoms, especially useful for methods development. Main reference: E. Smith, G. Evans, J. Foadi (2017) <doi:10.1088/1361-6404/aa8188>.
Author: James Foadi [cre, aut]
Maintainer: James Foadi <j.foadi@bath.ac.uk>

Diff between crone versions 0.1.0 dated 2019-07-27 and 0.1.1 dated 2019-08-24

 crone-0.1.0/crone/vignettes/BIBLIOGRAPHY.bib |only
 crone-0.1.1/crone/DESCRIPTION                |    8 ++---
 crone-0.1.1/crone/MD5                        |   39 +++++++++++++--------------
 crone-0.1.1/crone/NEWS.md                    |    5 ++-
 crone-0.1.1/crone/inst/doc/tutorial01.R      |    3 --
 crone-0.1.1/crone/inst/doc/tutorial01.Rnw    |   18 +++++++-----
 crone-0.1.1/crone/inst/doc/tutorial01.pdf    |binary
 crone-0.1.1/crone/inst/doc/tutorial02.pdf    |binary
 crone-0.1.1/crone/inst/doc/tutorial03.R      |    3 --
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 crone-0.1.1/crone/inst/doc/tutorial04.R      |    3 --
 crone-0.1.1/crone/inst/doc/tutorial04.Rnw    |   31 ++++++++++++---------
 crone-0.1.1/crone/inst/doc/tutorial04.pdf    |binary
 crone-0.1.1/crone/inst/doc/tutorial05.R      |    3 --
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 crone-0.1.1/crone/inst/doc/tutorial05.pdf    |binary
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 crone-0.1.1/crone/vignettes/tutorial03.Rnw   |   18 +++++++-----
 crone-0.1.1/crone/vignettes/tutorial04.Rnw   |   31 ++++++++++++---------
 crone-0.1.1/crone/vignettes/tutorial05.Rnw   |   23 +++++++++------
 21 files changed, 135 insertions(+), 109 deletions(-)

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New package citecorp with initial version 0.1.0
Package: citecorp
Type: Package
Title: Client for the Open Citations Corpus
Description: Client for the Open Citations Corpus (<http://opencitations.net/>). Includes a set of functions for getting one identifier type from another, as well as getting references and citations for a given identifier.
Version: 0.1.0
Authors@R: person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com", comment = c(ORCID = "0000-0003-1444-9135"))
License: MIT + file LICENSE
URL: https://github.com/ropenscilabs/citecorp
BugReports: https://github.com/ropenscilabs/citecorp/issues
Encoding: UTF-8
Imports: crul (>= 0.7.0), data.table, fauxpas, jsonlite
Suggests: testthat, vcr
RoxygenNote: 6.1.1
X-schema.org-applicationCategory: Literature
X-schema.org-keywords: doi, metadata, citation, opencitations, bibtex
X-schema.org-isPartOf: https://ropensci.org
NeedsCompilation: no
Packaged: 2019-08-23 19:33:57 UTC; sckott
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2019-08-24 14:20:07 UTC

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New package bikm1 with initial version 0.9.0
Package: bikm1
Type: Package
Title: Coclustering Adjusted Rand Index and Bikm1 Procedure for Contingency and Binary Data-Sets
Version: 0.9.0
Authors@R: person("Valerie", "Robert", email = "valerie.robert.math@gmail.com", role = c("aut", "cre"))
Maintainer: Valerie Robert <valerie.robert.math@gmail.com>
Description: Coclustering of the rows and columns of a contingency or binary matrix, or double binary matrices and model selection for the number of row and column clusters. Three models are considered: the Poisson latent block model for contingency matrix, the binary latent block model for binary matrix and a new model we develop: the multiple latent block model for double binary matrices. A new procedure named bikm1 is implemented to investigate more efficiently the grid of numbers of clusters. Then, the studied model selection criteria are the integrated completed likelihood (ICL) and the Bayesian integrated likelihood (BIC). Finally, the coclustering adjusted Rand index (CARI) to measure agreement between coclustering partitions is implemented. Robert Valerie and Vasseur Yann (2017) <arXiv:1705.06760>.
Imports: gtools, stats, graphics, grDevices, methods, parallel, ade4, pracma, ggplot2, reshape2, grid
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-24 07:33:33 UTC; valerierobert
Author: Valerie Robert [aut, cre]
Repository: CRAN
Date/Publication: 2019-08-24 14:30:02 UTC

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New package statsExpressions with initial version 0.1.0
Type: Package
Package: statsExpressions
Title: Expressions with Statistical Details
Version: 0.1.0
Authors@R: c(person(given = "Indrajeet", family = "Patil", role = c("cre", "aut", "ctb"), email = "patilindrajeet.science@gmail.com", comment = c(ORCID = "0000-0003-1995-6531")), person(given = "Chuck", family = "Powell", role = "ctb", email = "ibecav@gmail.com", comment = c(ORCID = "0000-0002-3606-2188")))
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Description: Statistical processing backend for 'ggstatsplot', this package creates expressions with details from statistical tests. Currently, it supports only the most common types of statistical tests: parametric, nonparametric, robust, and bayesian versions of t-test/anova, correlation analyses, contingency table analysis, and regression analyses.
License: GPL-3 | file LICENSE
URL: https://indrajeetpatil.github.io/statsExpressions/, https://github.com/IndrajeetPatil/statsExpressions
BugReports: https://github.com/IndrajeetPatil/statsExpressions/issues
Depends: R (>= 3.5.0)
Imports: BayesFactor (>= 0.9.12-4.2), boot (>= 1.3-22), broomExtra (>= 0.0.5), crayon (>= 1.3.4), dplyr (>= 0.8.3), ellipsis (>= 0.2.0.1), ez (>= 4.4-0), groupedstats, magrittr (>= 1.5), MCMCpack (>= 1.4-4), methods, psych, rcompanion (>= 2.2.2), rlang (>= 0.4.0), stats, tibble (>= 2.1.3), tidyr (>= 0.8.3), WRS2 (>= 1.0-0)
Suggests: ggplot2, knitr, purrr, rmarkdown, spelling, testthat
VignetteBuilder: knitr
Encoding: UTF-8
Language: en-US
LazyData: true
RoxygenNote: 6.1.1.9000
NeedsCompilation: no
Packaged: 2019-08-23 13:40:37 UTC; inp099
Author: Indrajeet Patil [cre, aut, ctb] (<https://orcid.org/0000-0003-1995-6531>), Chuck Powell [ctb] (<https://orcid.org/0000-0002-3606-2188>)
Repository: CRAN
Date/Publication: 2019-08-24 13:20:02 UTC

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New package MEDseq with initial version 1.0.0
Package: MEDseq
Type: Package
Date: 2019-08-23
Title: Mixtures of Exponential-Distance Models with Covariates
Version: 1.0.0
Authors@R: c(person("Keefe", "Murphy", email = "keefe.murphy@ucd.ie", role = c("aut", "cre")), person("Thomas Brendan", "Murphy", email = "brendan.murphy@ucd.ie", role = "ctb"), person("Raffaella", "Piccarreta", email = "raffaella.piccarreta@unibocconi.it ", role = "ctb"), person("Isobel Claire", "Gormley", email = "claire.gormley@ucd.ie", role = "ctb"))
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2019) <arXiv:1908.07963>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Depends: R (>= 3.3.0)
License: GPL (>= 2)
Encoding: UTF-8
URL: https://cran.r-project.org/package=MEDseq
BugReports: https://github.com/Keefe-Murphy/MEDseq
LazyData: true
Imports: cluster, matrixStats, nnet, seriation, stringdist, TraMineR, WeightedCluster
Suggests: knitr
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-23 12:49:30 UTC; Keefe
Author: Keefe Murphy [aut, cre], Thomas Brendan Murphy [ctb], Raffaella Piccarreta [ctb], Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Repository: CRAN
Date/Publication: 2019-08-24 13:10:02 UTC

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New package arcos with initial version 0.8.2
Package: arcos
Type: Package
Title: Load ARCOS Prescription Data Prepared by the Washington Post
Version: 0.8.2
Date: 2019-08-09
Authors@R: c( person(given="Steven", family="Rich", email="steven.rich@washpost.com",role=c("aut", "ctb")), person(given="Andrew", family="Ba Tran", email="andrew.tran@washpost.com", role=c("aut", "cre")), person(given="Aaron", family="Williams", email="aaron.williams@washpost.com", role=c("aut", "ctb")), person(given="Jason", family="Holt", email="jason.holt@washpost.com", role=c("ctb")), person(given="The Washington Post", role=c("cph")), person(given="The Charleston Gazette-Mail", role=c("cph")) )
URL: https://github.com/wpinvestigative/arcos
BugReports: https://github.com/wpinvestigative/arcos/issues
Description: A wrapper for the 'ARCOS API' <https://arcos-api.ext.nile.works/__swagger__/> that returns raw and summarized data frames from the Drug Enforcement Administration’s Automation of Reports and Consolidated Orders System, a database that monitors controlled substances transactions between manufacturers and distributors which was made public by The Washington Post and The Charleston Gazette-Mail.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.3.0)
Suggests: tidyverse, leaflet, knitr, sf, tigris, testthat (>= 2.1.0), rmarkdown, data.table, formattable, geofacet, lubridate, scales, viridis
Imports: stringr, magrittr, jsonlite, dplyr, urltools, vroom
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-23 15:25:16 UTC; trana
Author: Steven Rich [aut, ctb], Andrew Ba Tran [aut, cre], Aaron Williams [aut, ctb], Jason Holt [ctb], The Washington Post [cph], The Charleston Gazette-Mail [cph]
Maintainer: Andrew Ba Tran <andrew.tran@washpost.com>
Repository: CRAN
Date/Publication: 2019-08-24 13:30:02 UTC

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New package HBV.IANIGLA with initial version 0.1.0
Package: HBV.IANIGLA
Type: Package
Title: Decoupled Hydrological Model for Research and Education Purposes
Version: 0.1.0
Date: 2019-08-16
Author: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Maintainer: Ezequiel Toum <etoum@mendoza-conicet.gob.ar>
Description: The HBV (Hydrologiska Byråns Vattenbalansavdelning) hydrological model is decoupled to allow the user to build his/her own model. This version was developed by the author in IANIGLA-CONICET (Instituto Argentino de Nivologia, Glaciologia y Ciencias Ambientales - Consejo Nacional de Investigaciones Cientificas y Tecnicas) for hydroclimatic studies in the Andes. HBV.IANIGLA incorporates modules for precipitation and temperature interpolation, and also for clean and debris covered ice melt estimations.
License: GPL (>= 3)
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.0)
LinkingTo: Rcpp
RoxygenNote: 6.1.1
NeedsCompilation: yes
Packaged: 2019-08-23 12:52:16 UTC; ezequiel
Repository: CRAN
Date/Publication: 2019-08-24 13:00:02 UTC

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New package phonfieldwork with initial version 0.0.1
Package: phonfieldwork
Type: Package
Title: Linguistic Phonetic Fieldwork Tools
Version: 0.0.1
Depends: R (>= 3.5.0)
Imports: tuneR, rmarkdown
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Description: There are a lot of different typical tasks that should be solved during phonetic research and experiments, such as creation of presentation that will contain all stimuli, rename and concatenate multiple sound files recorded during phonetic session, automatically annotate 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Paul Boersma, David Weenink 2018 <http://www.fon.hum.uva.nl/praat/>), create an html that includes annotation and spectrogram tables, convert multiple formats ('Praat' TextGrid, 'EXMARaLDA' and 'ELAN') into each other. All those tasks could be solved by mixture of different tools (some programs in any programming language for automatic renaming, some Praat scripts for the file concatenation and renaming, etc). This package provides functionality that will make it easier to solve those tasks independently of any of tools. You could also compare the functionality with other packages: 'rPraat' <https://CRAN.R-project.org/package=rPraat>, 'textgRid' <https://CRAN.R-project.org/package=textgRid>.
License: GPL (>= 2)
URL: https://CRAN.R-project.org/package=phonfieldwork
BugReports: https://github.com/agricolamz/phonfieldwork/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-23 11:04:42 UTC; agricolamz
Repository: CRAN
Date/Publication: 2019-08-24 11:10:03 UTC

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New package sprintr with initial version 0.9.0
Package: sprintr
Type: Package
Title: Sparse Reluctant Interaction Modeling
Version: 0.9.0
Date: 2019-08-08
Authors@R: person("Guo", "Yu", email = "gy63@uw.edu", role = c("aut", "cre"))
Description: An implementation of a computationally efficient method to fit large-scale interaction models based on the reluctant interaction selection principle. The method and its properties are described in greater depth in Yu, G., Bien, J., and Tibshirani, R.J. (2019) "Reluctant interaction modeling", which is available at <arXiv:1907.08414>.
BugReports: https://github.com/hugogogo/sprintr/issues
License: GPL-3
Imports: Rcpp (>= 0.12.16), glmnet
LinkingTo: Rcpp, RcppArmadillo
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2019-08-23 01:16:15 UTC; hugo
Author: Guo Yu [aut, cre]
Maintainer: Guo Yu <gy63@uw.edu>
Repository: CRAN
Date/Publication: 2019-08-24 10:40:02 UTC

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New package idiogramFISH with initial version 1.0.0
Package: idiogramFISH
Title: Idiograms with Marks and Karyotype Indices
Version: 1.0.0
Date: 2019-08-18
Authors@R: c(person("Fernando", "Roa", email = "froao@unal.edu.co", role = c("aut", "cre") ), person(given="Mariana PC Telles", email = "", role = c("ctb")) )
Description: Plot idiograms of several karyotypes having a set of dataframes for chromosome data and optionally mark data. Includes also a function to plot holocentrics and its marks supporting micrometers and Mb. Marks can have square or dot form, its legend (label) can be drawn inline or to the right of karyotypes. It is possible to calculate chromosome indices by Levan et al. (1964) <doi:10.1111/j.1601-5223.1964.tb01953.x> , karyotype indices of Watanabe et al. (1999) <doi:10.1007/PL00013869> and Romero-Zarco (1986) <doi:10.2307/1221906> and classify chromosomes by morphology Guerra (1986) and Levan et al. (1964).
Depends: R (>= 3.0)
Imports: crayon, knitr
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Suggests: rmarkdown
VignetteBuilder: knitr
URL: https://ferroao.gitlab.io/manualidiogramfish/
BugReports: https://gitlab.com/ferroao/idiogramFISH/issues
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-22 22:01:55 UTC; fernando
Author: Fernando Roa [aut, cre], Mariana PC Telles [ctb]
Maintainer: Fernando Roa <froao@unal.edu.co>
Repository: CRAN
Date/Publication: 2019-08-24 10:20:03 UTC

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New package AzureVMmetadata with initial version 1.0.0
Package: AzureVMmetadata
Title: Interface to Azure Virtual Machine Instance Metadata
Version: 1.0.0
Authors@R: c( person("Hong", "Ooi", , "hongooi@microsoft.com", role = c("aut", "cre")), person("Microsoft", role="cph") )
Description: A simple interface to the instance metadata for a virtual machine running in Microsoft's 'Azure' cloud. This provides information about the VM's configuration, such as its processors, memory, networking, storage, and so on. Part of the 'AzureR' family of packages.
URL: https://github.com/Azure/AzureVMmetadata https://github.com/Azure/AzureR
BugReports: https://github.com/Azure/AzureVMmetadata/issues
License: MIT + file LICENSE
Depends: R (>= 3.3)
Imports: openssl, httr (>= 1.3)
Suggests: AzureAuth, AzureVM
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2019-08-23 01:00:06 UTC; hongo
Author: Hong Ooi [aut, cre], Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Repository: CRAN
Date/Publication: 2019-08-24 10:40:05 UTC

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New package dbflobr with initial version 0.0.1
Package: dbflobr
Title: Read and Write Files to SQLite Databases
Version: 0.0.1
Authors@R: c( person("Sebastian", "Dalgarno", , "seb@poissonconsulting.ca", c("aut", "cre"), comment = c(ORCID = "0000-0002-3658-4517")), person("Joe", "Thorley", , "joe@poissonconsulting.ca", "aut", comment = c(ORCID = "0000-0002-7683-4592")), person("Poisson Consulting", role = c("cph", "fnd")) )
Description: Reads and writes files to SQLite databases <https://www.sqlite.org/index.html> as flobs (a flob is a blob that preserves the file extension).
License: MIT + file LICENSE
Imports: checkr, flobr, glue, DBI, RSQLite
Suggests: testthat, covr
URL: https://github.com/poissonconsulting/dbflobr
BugReports: https://github.com/poissonconsulting/dbflobr/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2019-08-22 18:37:34 UTC; sebastiandalgarno
Author: Sebastian Dalgarno [aut, cre] (<https://orcid.org/0000-0002-3658-4517>), Joe Thorley [aut] (<https://orcid.org/0000-0002-7683-4592>), Poisson Consulting [cph, fnd]
Maintainer: Sebastian Dalgarno <seb@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2019-08-24 09:20:02 UTC

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Package BayesX updated to version 0.3-1 with previous version 0.3-0 dated 2018-05-18

Title: R Utilities Accompanying the Software Package BayesX
Description: Functions for exploring and visualising estimation results obtained with BayesX, a free software for estimating structured additive regression models (<http://www.BayesX.org>). In addition, functions that allow to read, write and manipulate map objects that are required in spatial analyses performed with BayesX.
Author: Nikolaus Umlauf [aut, cre], Thomas Kneib [aut], Nadja Klein [aut], Felix Heinzl [ctb], Andreas Brezger [ctb], Daniel Sabanes Bove [ctb]
Maintainer: Nikolaus Umlauf <Nikolaus.Umlauf@uibk.ac.at>

Diff between BayesX versions 0.3-0 dated 2018-05-18 and 0.3-1 dated 2019-08-24

 DESCRIPTION           |    8 ++++----
 MD5                   |    8 ++++----
 R/drawmap.R           |    9 +++++----
 man/BayesX-package.Rd |   12 ++++++++----
 man/fuse.Rd           |    4 ++--
 5 files changed, 23 insertions(+), 18 deletions(-)

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Package dLagM updated to version 1.0.17 with previous version 1.0.15 dated 2019-07-18

Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>

Diff between dLagM versions 1.0.15 dated 2019-07-18 and 1.0.17 dated 2019-08-24

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Package summarytools updated to version 0.9.4 with previous version 0.9.3 dated 2019-04-11

Title: Tools to Quickly and Neatly Summarize Data
Description: Data frame summaries, cross-tabulations, weight-enabled frequency tables and common univariate statistics in concise tables available in a variety of formats (plain ASCII, Markdown and HTML). A good point-of-entry for exploring data, both for experienced and new R users.
Author: Dominic Comtois [aut, cre]
Maintainer: Dominic Comtois <dominic.comtois@gmail.com>

Diff between summarytools versions 0.9.3 dated 2019-04-11 and 0.9.4 dated 2019-08-24

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New package gripp with initial version 0.2.20
Package: gripp
Type: Package
Title: General Inverse Problem Platform
Version: 0.2.20
Author: Jader Lugon Junior, Antonio Jose da Silva Neto
Maintainer: Jader Lugon Junior <jlugonjr@gmail.com>
Description: Set of functions designed to solve inverse problems. The direct problem is used to calculate a cost function to be minimized. Here are listed some papers using Inverse Problems solvers and sensitivity analysis: (Jader Lugon Jr.; Antonio J. Silva Neto 2011) <doi:10.1590/S1678-58782011000400003>. (Jader Lugon Jr.; Antonio J. Silva Neto; Pedro P.G.W. Rodrigues 2008) <doi:10.1080/17415970802082864>. (Jader Lugon Jr.; Antonio J. Silva Neto; Cesar C. Santana 2008) <doi:10.1080/17415970802082922>.
Depends: R (>= 2.10)
Imports: utils, usethis, GenSA, GA
License: GPL-3
Encoding: UTF-8
LazyData: true
Repository: CRAN
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2019-08-23 22:48:55 UTC; Usuario
Date/Publication: 2019-08-24 05:30:02 UTC

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Package Patterns updated to version 1.1 with previous version 1.0 dated 2019-06-07

Title: Deciphering Biological Networks with Patterned Heterogeneous Measurements
Description: A modeling tool dedicated to biological network modeling. It allows for single or joint modeling of, for instance, genes and proteins. It starts with the selection of the actors that will be the used in the reverse engineering upcoming step. An actor can be included in that selection based on its differential measurement (for instance gene expression or protein abundance) or on its time course profile. Wrappers for actors clustering functions and cluster analysis are provided. It also allows reverse engineering of biological networks taking into account the observed time course patterns of the actors. Many inference functions are provided and dedicated to get specific features for the inferred network such as sparsity, robust links, high confidence links or stable through resampling links. Some simulation and prediction tools are also available for cascade networks. Example of use with microarray or RNA-Seq data are provided.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>)
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>

Diff between Patterns versions 1.0 dated 2019-06-07 and 1.1 dated 2019-08-24

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Package Cascade updated to version 1.8 with previous version 1.7 dated 2019-02-18

Title: Selection, Reverse-Engineering and Prediction in Cascade Networks
Description: A modeling tool allowing gene selection, reverse engineering, and prediction in cascade networks. Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014) <doi:10.1093/bioinformatics/btt705>.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>), Laurent Vallat [ctb], Nicolas Jung [ctb]
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>

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